rs765661419
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000170.3(GLDC):c.2310C>T(p.Ile770=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000618 in 1,455,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. I770I) has been classified as Likely benign.
Frequency
Consequence
NM_000170.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLDC | NM_000170.3 | c.2310C>T | p.Ile770= | synonymous_variant | 19/25 | ENST00000321612.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLDC | ENST00000321612.8 | c.2310C>T | p.Ile770= | synonymous_variant | 19/25 | 1 | NM_000170.3 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249682Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134892
GnomAD4 exome AF: 0.00000618 AC: 9AN: 1455192Hom.: 0 Cov.: 30 AF XY: 0.00000552 AC XY: 4AN XY: 724080
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Non-ketotic hyperglycinemia Uncertain:1Benign:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Feb 13, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at